DEanalysis_kfish_osmotic
Lisa Johnson
2019-04-30
#Setting a reasonable p-value threshold to be used throughout
p_cutoff <- 0.05
p_cutoff_new <- 0.05
knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE)
FC_cutoff_original <- 0
FC_cutoff_new <- 11 Global parameters for modeling
## R version 3.5.2 (2018-12-20)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS High Sierra 10.13.3
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] vsn_3.50.0 lattice_0.20-38
## [3] gplots_3.0.1.1 edgeR_3.24.3
## [5] limma_3.38.3 DESeq2_1.22.2
## [7] SummarizedExperiment_1.12.0 DelayedArray_0.8.0
## [9] BiocParallel_1.16.6 matrixStats_0.54.0
## [11] Biobase_2.42.0 GenomicRanges_1.34.0
## [13] GenomeInfoDb_1.18.2 IRanges_2.16.0
## [15] S4Vectors_0.20.1 BiocGenerics_0.28.0
## [17] ggrepel_0.8.0 tidyr_0.8.3
## [19] dplyr_0.8.0.1 RColorBrewer_1.1-2
## [21] cowplot_0.9.4 pheatmap_1.0.12
## [23] gtools_3.8.1 ggplot2_3.1.1
## [25] MASS_7.3-51.4
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-6 bit64_0.9-7 tools_3.5.2
## [4] backports_1.1.4 affyio_1.52.0 R6_2.4.0
## [7] KernSmooth_2.23-15 rpart_4.1-13 Hmisc_4.2-0
## [10] DBI_1.0.0 lazyeval_0.2.2 colorspace_1.4-1
## [13] nnet_7.3-12 withr_2.1.2 tidyselect_0.2.5
## [16] gridExtra_2.3 preprocessCore_1.44.0 bit_1.1-14
## [19] compiler_3.5.2 htmlTable_1.13.1 caTools_1.17.1.2
## [22] scales_1.0.0 checkmate_1.9.1 affy_1.60.0
## [25] genefilter_1.64.0 stringr_1.4.0 digest_0.6.18
## [28] foreign_0.8-71 rmarkdown_1.12 XVector_0.22.0
## [31] base64enc_0.1-3 pkgconfig_2.0.2 htmltools_0.3.6
## [34] htmlwidgets_1.3 rlang_0.3.4 rstudioapi_0.10
## [37] RSQLite_2.1.1 acepack_1.4.1 RCurl_1.95-4.12
## [40] magrittr_1.5 GenomeInfoDbData_1.2.0 Formula_1.2-3
## [43] Matrix_1.2-17 Rcpp_1.0.1 munsell_0.5.0
## [46] stringi_1.4.3 yaml_2.2.0 zlibbioc_1.28.0
## [49] plyr_1.8.4 grid_3.5.2 blob_1.1.1
## [52] gdata_2.18.0 crayon_1.3.4 splines_3.5.2
## [55] annotate_1.60.1 locfit_1.5-9.1 knitr_1.22
## [58] pillar_1.3.1 geneplotter_1.60.0 XML_3.98-1.19
## [61] glue_1.3.1 evaluate_0.13 latticeExtra_0.6-28
## [64] BiocManager_1.30.4 data.table_1.12.2 gtable_0.3.0
## [67] purrr_0.3.2 assertthat_0.2.1 xfun_0.6
## [70] xtable_1.8-3 survival_2.44-1.1 tibble_2.1.1
## [73] AnnotationDbi_1.44.0 memoise_1.1.0 cluster_2.0.8Number of raw counts, samples
## [1] 30471 130## [1] 5 81## [1] 30466 81## [1] "physiologyFW"
## [2] "physiologyM"
## [3] "condition15_ppt"
## [4] "cladeClade2"
## [5] "cladeClade3"
## [6] "physiologyM:condition15_ppt"
## [7] "physiologyM:cladeClade2"
## [8] "physiologyM:cladeClade3"
## [9] "condition15_ppt:cladeClade2"
## [10] "condition15_ppt:cladeClade3"
## [11] "physiologyM:condition15_ppt:cladeClade2"
## [12] "physiologyM:condition15_ppt:cladeClade3"## [1] 12
## attr(,"method")
## [1] "tolNorm2"
## attr(,"useGrad")
## [1] FALSE
## attr(,"tol")
## [1] 1.798561e-14## [1] 81 12## [1] "matrix"## [1] 21401 81
## [1] 0.751381## [1] "physiologyFW"
## [2] "physiologyM"
## [3] "condition15_ppt"
## [4] "cladeClade2"
## [5] "cladeClade3"
## [6] "physiologyM:condition15_ppt"
## [7] "physiologyM:cladeClade2"
## [8] "physiologyM:cladeClade3"
## [9] "condition15_ppt:cladeClade2"
## [10] "condition15_ppt:cladeClade3"
## [11] "physiologyM:condition15_ppt:cladeClade2"
## [12] "physiologyM:condition15_ppt:cladeClade3"2 Exploratory Plots
2.1 Heatmaps
2.1.1 Individuals clustered by overall expression
2.1.2 Individuals by Top 100 genes heatmap
2.1.3 Individuals clustered by top 100 gene expression
2.1.4 PCA for overall expression
